It's amazing to me how many people obsess over insect imitations, but don't seem to consider the range of prey species available when it comes to flats species. Perhaps it's because a shrimp, crab or baitfish will generally cover most bases. But anyone who's ever fished the flats has experienced inexplicable refusals on seemingly perfect presentations. And I'm not just talking about permit and bastards, it happens even with the "easy" species.
I'm sure there's an element of conditioning that happens with this. For example, if the bonefish flies you see all follow the Charlie/Gotcha profile that become imprinted as the format for a bonefish fly. Those patterns then get used more often and not necessarily because they are more effective flies in a given situation, but through confidence and sheer incumbency. Most of the time that's fine, but I think there's good reason to have some alternatives in the box. When I go on a trip like to take plenty of (too many) flies in a feeder box, like a Plano, then carry just a single box on the water. Each evening it's nothing to top up or adjust the contents to suit, so it's nothing to give a row to the more specialist patterns that imitate the various foodstuffs our target species will be foraging for.
In the spring I sent Johan Friberg some of my clone worms and hooligan crabs to try out, in return he sent me a batch of his Nubian Spaghetti, a small worm fly that has been destroying everything on the Red Sea flats of Sudan. They'll be in my Okinawa box next to some clam imitations and urchins. For me these patterns aren't just there as a last resort, I'm happy fishing them from the get-go. Others might need a bit of time and some success to become confident in them, which is probably best done on days when things just seem to be going right. But I think it's worth the effort so you can have something up your sleeve for the days when they won't eat a clouser or just when the usual stuff isn't necessarily the best option available